Maintained by Robin Tecon, microbiologist and postdoctoral researcher at the Swiss Federal Institute of Technology Zürich. This blog is about bacteria (and other microbes) and the scientists who study them.

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Saturday, September 22, 2012

In the first part of this post, I insisted on living organisms
(viruses, bacteria, eukaryotes) and their evolutionary history.

Here I want to
look at what Koonin writes about the mechanism of evolution.

What drives evolution?

One central idea in Koonin’s book, I think, is to propose an
evolutionary outlook that is based on an analogy with the physical world. Central,
for instance, is stochasticity, as a force shaping the genomic evolution. Equally
important, in Koonin’s view, are the statistical principles that govern the
interactions between all genes within a genome (he likens the collection of all
genes in a genome to the ideal gas model in physics). Thus, genes are
influenced by a number of statistical rules. On this line, even though it is
apparently not possible to define “laws of genomics”, certain regularities can
be identified, such as the proportion of different functional classes of genes
within a given prokaryotic genome.

Koonin writes, p. 405:

“it is remarkable that the advances of genomics and systems
biology, while revealing an extremely complex, multifaceted picture of
evolution, at the same time allow us to derive powerful and simplifying
generalizations. It is tempting to offer yet another version of the famous
phrase: Nothing in evolution—and in population genetics—makes sense except in light of
statistical physics.”

Sunday, September 16, 2012

About fifteen years ago, a revolution started in the
biological sciences, which goes by the name whole
genome sequencing. I don’t have memories of the announcement of the first
bacterial genome in 1995 (I was in high school and not really following biology
news…), but at the time of the human genome project I was a biology student at
the University and I remember very well when the paper describing the human
genome came out in 2001 (we had to read it in class!).

Until recently, my feeling about whole genome sequencing was
that it was a technical revolution, not a conceptual one. After all, I thought,
the sequence information revolution already took place in the seventies, when
Carl Woese pioneered the use of 16S ribosomal RNA to construct phylogeny.

I revised this feeling, thanks in part to the excellent book
of Eugene Koonin, The Logic of Chance
(2011)—subtitled
the nature and origin of biological
evolution—and published by Financial Times Press (yes, they do have a
science catalog!).

Sunday, September 09, 2012

Here, for a change, I want to wander into philosophical
territory. I should first admit that I am rather ignorant of it, since I never
studied philosophy past the high school level. But my interest remained vivid
and I read philosophical books regularly. More important, I believe that every
scientist has to keep an eye – even if it is half-open – on philosophy. Isn’t science
the daughter of philosophy? (After all, science used to be “natural philosophy”.)
And ironically, aren’t I a doctor in philosophy (Ph.D.)?

One year ago I was talking about philosophy with a colleague
in the lab (although I can’t remember how the discussion drifted to this topic!).
At some point my colleague said that he couldn’t find any use in philosophy,
and this baffled me. I mentioned the philosophy of science and Karl Popper as a
counter example, but retrospectively I didn’t need to be so specific.
Philosophy is important per se— if
it has practical applications for scientists it is a good thing but not its
final goal.

Nonetheless, I started thinking about examples of
philosophical inquiries that have repercussions in the day-to-day life of
scientists, and I realized there’s plenty. Here I would like to share one which
I think is essential: the reflection on nature and natural phenomena.